I chatted with Jelica C at QB support today about this because we have the same question. She wrote the following:
Alright, as I double check here I can see that markup is not
an option when we try to customize your report.
The only available columns we can add are the options
we see when we click on Customize report then under
display Tab under columns those are the only information we can include.
I do apologize but for now, that is not yet possible.
But I already take note of that so that our
product engineer can work on this to be available.
I also called support and spoke with rep John Bernard who also mentioned that although we can export a report (or Transaction Journal showing the details of the estimate), we cannot export the Estimate itself and since when we turn an Estimate into a form of report (I turn them into Transaction Journals in order to export them), we lose the ability to have the Markup column show up.
Hope that's helpful.